A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object

In current biomedical and complex trait research, increasing numbers of large molecular profiling (omics) data sets are being generated. At the same time, many studies fail to be reproduced (Baker 2016, Kim 2018). In order to improve study reproducibility and data reuse, including integration of data sets of different types and origins, it is imperative to work with omics data that is findable, accessible, interoperable, and reusable (FAIR, Wilkinson 2016) at the source. The data analysis, integration and stewardship pillar of the Netherlands X-omics Initiative aims to facilitate multi-omics research by providing tools to create, analyze and integrate FAIR omics data. We here report a joint activity of X-omics and the Netherlands Twin Register demonstrating the FAIRification of a multi-omics data set and the development of a FAIR multi-omics data analysis workflow.

The implementation of FAIR principles (Wilkinson 2016) can improve scientific transparency and facilitate data reuse. However, Kim (2018) showed in a case study that the availability of data and code are required but not sufficient to reproduce data analyses. They highlighted the importance of interoperable and open formats, and structured metadata. In order to increase research reproducibility on the data analysis level, additional practices such as version-control, code licensing, and documentation have been proposed. These include recommendations for FAIR software by the Netherlands eScience Center and the Dutch Data Archiving and Networked Services (DANS), and FAIR principles for research software proposed by the Research Data Alliance (Chue Hong 2022). Data analysis in biomedical research usually comprises multiple steps often resulting in complex data analysis workflows and requiring additional practices, such as containerization, to ensure transparency and reproducibility (Goble 2020, Stoudt 2021).

We apply these practices to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies, see consortium members in Suppl. material 1) (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant or discordant for childhood aggression. The ACTION-Curium-LUMC cohort consists of children referred to the Dutch LUMC Curium academic center for child and youth psychiatry. With the joint analysis of multi-omics data and behavioral data, we aim to identify substructures in the ACTION-NTR cohort and link them to aggressive behavior. First, the individuals are clustered using Similarity Network Fusion (SNF, Wang 2014), and latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) (Argelaguet 2018) and Multiple Correspondence Analysis (MCA, Lê 2008, Husson 2017). In a second step, we determine correlations between -omics and phenotype dimensions, and use them to explain the subgroups of individuals from the ACTION-NTR cohort. In order to validate the results, we project data of the ACTION-Curium-LUMC cohort onto the latent dimensions and determine if correlations between omics and phenotype data can be reproduced.

Integration of data across cohorts and across data types, requires interoperability. We applied different practices to make the data FAIR, including conversion of files to community-standard formats, and capturing experimental metadata using the ISA (Investigation, Study, Assay) metadata framework (Johnson 2021) and ontology-based annotations. All data analysis steps including pre-processing of different omics data types were implemented in either R or Python and combined in a modular Nextflow (Di Tommaso 2017) workflow, where the environment for each step is provided as a Singularity (Kurtzer 2017) container. The analysis workflow is packaged in a Research Object Crate (RO-Crate) (Soiland-Reyes 2022). The RO-Crate is a FAIR digital object that contains the Nextflow workflow including ontology-based annotations of each analysis step. Since omics data is considered to be potentially personally identifiable, the packaged workflow contains a minimal synthetic data set resembling the original data structure. Finally, the code is made available on GitHub and the workflow is registered at Workflowhub (Goble 2021). Since our Nextflow workflow is set up in a modular manner, the individual analysis steps can be reused in other workflows. We demonstrate this replicability by applying different sub-workflows to data from two different cohorts.